Table 1.
Gene differences between C. rodentium strains EX-33 and ICC168.
Figure 1.
Comparison of the genome of C. rodentium with related bacteria.
Genome comparison of the DNA sequences of C. rodentium ICC168 (middle) with E. coli K12 MG1655 (U00096, top) and Salmonella Typhimurium LT2 (AE006468, bottom). Grey shading between two genomes indicates regions of nucleotide similarity (BLASTN matches with a minimum length of 1000 bp) between sequences on the same strand, green shading highlights where the matching sequences are inverted with respect to each other (percentage identity is indicated). The locations of IS elements in the C. rodentium genome are shown as blue bars. An orange pointer indicates the origin of replication (oriC) in the E. coli genome. The GC Deviation (G−C)/(G+C) plot is shown above each genome (window size 1000 bp) with the switch in GC deviation in C. rodentium highlighted by red shading. The scale bar indicates genome length. This figure was produced using Easyfig [67].
Table 2.
Classification and location of IS elements in C. rodentium.
Figure 2.
PFGE profile of different C. rodentium isolates.
PFGE generated after XbaI cleavage of genomic DNA isolated from different strains and isolates of C. rodentium. Strain ICC168 shows the same PFGE pattern as for ICC169, ICC169-474, ICC169-335 and ICC169-476. Two isolates displayed significant differences in their PFGE profiles (indicated by red arrows); ICC169-407 has a band missing at approximately 340 kb and additional bands of approximately 280 kb and 420 kb; ICC169-496 is also missing the 340 kb band and has two extra bands between 145 and 200 kb. Markers are from New England BioLabs. Band sizes are indicated in kb.
Table 3.
Bacterial strains used in this study.
Figure 3.
Chromosomal rearrangements identified in C. rodentium isolates ICC169-407 and ICC169-496.
Deviations from (A) the sequence of the wild-type strain ICC168, are depicted. Rearrangements are highlighted in red and show: (B) genomic inversion between two copies of ISCro4; (C) genomic inversion between two identical sequences encoding Elongation factor Tu; (D) genomic inversion between identical repeat sequences encoding the T3SS effector NleD and an adjacent transposase; (E) translocation of sequence from one location to another due to recombination between identical sequences in two Rhs elements. The GC deviation (G−C)/(G+C) plot for each genome orientation is shown above each sequence.
Figure 4.
Genetic organisation of the C. rodentium prophages showing transcriptionally active genes.
The genomes of each of the five intact prophages in the C. rodentium genome are shown aligned with mapped sequence reads for the whole genome transcriptome. The prophage remnant CRPr20 is also included due to its high similarity to CRP38 and the difficulty in mapping repetitive sequences. The RNA-seq data are represented as a plot showing the depth of sequences mapped to the forward strand (blue) and reverse strand (red) above each genome (window size = 200 bp). The majority of prophage genes, including those predicted to encode phage structural and lysis genes (see key), are expressed. Putative cargo genes can be identified by their relatively high levels of expression (numbered CDSs; see Table 4 for details). The scale bar indicates genome length. This figure was produced using Easyfig [67] and Artemis [68].
Table 4.
Highly expressed putative phage cargo genes.
Figure 5.
Electron micrographs of ΦNP negatively stained with phosphotungstic acid.
All virions can be seen with contracted tails. Bars, 100 nm (top panels), 200 nm (bottom panel).
Figure 6.
Mouse shedding of C. rodentium.
Bacterial shedding in mouse faeces was monitored over the course of infection from individual mice. The mean count and standard deviation from groups of five mice infected with different C. rodentium isolates (see key) are shown.
Figure 7.
PFGE of XbaI-digested C. rodentium genomic DNA from isolates recovered before and after mouse inoculation.
(A) PFGE profile of isolate ICC169-496 pre mouse inoculation (left) and isolate ICC169-496c10 recovered from mouse faeces 10 days post inoculation. (B) PFGE profile of isolate ICC169-407b15 recovered from mouse faeces 15 days post inoculation (left) compared to that of the infecting isolate ICC169-407 pre mouse inoculation (right). (C) PFGE profile of the pre mouse inoculation strain ICC180 compared to that for ICC180-P10 recovered from faeces after 10 passages though the mouse. Additional/missing bands are indicated by red arrows.